We analysed whole genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. 93 protein-coding cancer genes carried likely driver mutations. Some non-coding regions exhibited high mutation frequencies but most have distinctive structural features probably causing elevated mutation rates and do not harbour driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed 12 base substitution and six rearrangement signatures. Three rearrangement signatures, characterised by tandem duplications or deletions, appear associated with defective homologous recombination based DNA repair: one with deficient BRCA1 function; another with deficient BRCA1 or BRCA2 function; the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operative, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.

The pan-cancer analysis of whole genomes The expansion of whole-genome sequencing studies from individual ICGC and TCGA working groups presented the opportunity to undertake a meta-analysis of genomic features across tumour types. To achieve this, the PCAWG Consortium was established. A Technical Working Group implemented the informatics analyses by aggregating the raw sequencing data from different working groups that studied individual tumour types, aligning the sequences to the human genome and delivering a set of high-quality somatic mutation calls for downstream analysis (Extended Data Fig. 1). Given the recent meta-analysis

Somatic cells acquire mutations throughout the course of an individual’s life. Mutations occurring early in embryogenesis will often be present in a substantial proportion of, but not all, cells in the post-natal human and thus have particular characteristics and impact1. Depending upon their location in the genome and the proportion of cells they are present in, these mosaic mutations can cause a wide range of genetic disease syndromes2 and predispose to cancer3,4. They have a high chance of being transmitted to offspring as de novo germline mutations and, in principle, can provide insights into early human embryonic cell lineages and their contributions to adult tissues5. Although it is known that gross chromosomal abnormalities are remarkably common in early human embryos6 our understanding of early embryonic somatic mutations is very limited. Here, we use whole genome sequences of adult normal blood from 241 individuals to identify 163 early embryonic mutations. We estimate that approximately three base substitution mutations occur per cell per cell-doubling in early human embryogenesis and these are mainly attributable to two known mutational signatures7. We used the mutations to reconstruct developmental lineages of adult cells and demonstrate that the two daughter cells of many early embryonic cell doublings contribute asymmetrically to adult blood at an approximately 2:1 ratio. This study therefore provides insights into the mutation rates, the mutational processes and the developmental outcomes of cell dynamics operative during early human embryogenesis.

Triple-negative breast cancer, defined as that with negative expression of estrogen and progesterone receptors and cerbB2, accounted for 11% of invasive breast cancers in our study, drawn from an original cohort of 7048 women diagnosed with breast cancer from the files of the Department of Pathology, Singapore General Hospital, over 14 years. Women with triple-negative breast cancer were generally postmenopausal, with adverse pathological characteristics of high histological grade and frequent nodal metastases. Using a set of 61 invasive breast cancers earlier profiled into molecular subtypes with expression arrays, we defined specificity and sensitivity values for different immunohistochemical panels of basal keratins (CK5/6, CK14, CK17, 34 beta E12), CD117, EGFR, p63 and SMA in defining basal-like breast cancer. Subsequent application of a tri-panel of CK14, EGFR and 34 beta E12 (specificity 100% and sensitivity 78%) to our group of 653 triple-negative breast cancers delineated 84% to be basal-like. Immunohistochemical expression of individual biological markers correlated with unfavorable pathological parameters. We conclude that triple-negative breast cancers in an Asian population harbor adverse pathobiological features, and an immunohistochemical surrogate panel can be reliably used to define basal-like cancers among them.